| shazam-package | The shazam package |
| Baseline | S4 class defining a BASELINe (selection) object |
| Baseline-class | S4 class defining a BASELINe (selection) object |
| calcBaseline | Calculate the BASELINe PDFs |
| calcDBExpectedMutations | Calculate expected mutation frequencies |
| calcDBObservedMutations | Calculate observed numbers of mutations |
| calcExpectedMutations | Calculate expected mutation frequencies of a sequence |
| calcObservedMutations | Count the number of observed mutations in a sequence. |
| calcTargetingDistance | Calculates a 5-mer distance matrix from a TargetingModel object |
| CHARGE_MUTATIONS | Amino acid mutation definitions |
| clearConsole | Clears the console |
| collapseByClone | Identifies clonal consensus sequences |
| createBaseline | Creates a Baseline object |
| createMutabilityMatrix | Builds a mutability model |
| createMutationDefinition | Creates a MutationDefinition |
| createRegionDefinition | Creates a RegionDefinition |
| createSubstitutionMatrix | Builds a substitution model |
| createTargetingMatrix | Calculates a targeting rate matrix |
| createTargetingModel | Creates a TargetingModel |
| distToNearest | Distance to nearest neighbor |
| extendMutabilityMatrix | Extends a mutability model to include Ns. |
| extendSubstitutionMatrix | Extends a substitution model to include Ns. |
| getBaselineStats | Gets the summary statistics of a Baseline object |
| getnproc | Determines the numbers of CPU cores available |
| getPlatform | Determines the OS platform being used |
| groupBaseline | Group BASELINe PDFs |
| HS1FDistance | Human single nucleotide distance matrix. |
| HS5FModel | Human 5-mer targeting model. |
| HYDROPATHY_MUTATIONS | Amino acid mutation definitions |
| IMGT_SCHEMES | IMGT unique numbering schemes |
| IMGT_V | IMGT unique numbering schemes |
| IMGT_V_BY_REGIONS | IMGT unique numbering schemes |
| IMGT_V_BY_REGIONS_NO_CDR3 | IMGT unique numbering schemes |
| IMGT_V_NO_CDR3 | IMGT unique numbering schemes |
| InfluenzaDb | Example Change-O database |
| M1NDistance | Mouse single nucleotide distance matrix. |
| MutationDefinition | S4 class defining replacement and silent mutation definitions |
| MutationDefinition-class | S4 class defining replacement and silent mutation definitions |
| MUTATION_SCHEMES | Amino acid mutation definitions |
| plotBaselineDensity | Plots BASELINe probability density functions |
| plotBaselineSummary | Plots BASELINe summary statistics |
| plotMutability | Plot mutability probabilities |
| POLARITY_MUTATIONS | Amino acid mutation definitions |
| RegionDefinition | S4 class defining a region definition |
| RegionDefinition-class | S4 class defining a region definition |
| shazam | The shazam package |
| summarizeBaseline | Calculate BASELINe summary statistics |
| TargetingModel | S4 class defining a targeting model |
| TargetingModel-class | S4 class defining a targeting model |
| U5NModel | Uniform 5-mer targeting model. |
| writeTargetingDistance | Write targeting model distances to a file |